Contacts of the helix formed by residues 341 - 355 (chain D) in PDB entry 1T5A
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 341 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B GLN* 2.8 27.1 - - - +
332B GLU* 4.5 17.7 - - + -
344B GLU* 5.1 4.8 + - - +
333D SER* 3.5 17.9 - - - +
340D PRO* 1.3 77.5 - - - +
342D ARG* 1.3 63.0 + - - +
343D ALA* 3.3 8.6 + - - +
344D GLU* 2.9 47.1 + - - +
345D GLY* 3.1 17.2 + - - -
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Residues in contact with ARG 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP* 3.7 14.3 + - - -
294B ARG* 2.7 56.1 + - + +
295B GLY 2.9 20.1 + - - +
298B GLY* 3.3 17.9 + - - -
299B ILE* 3.5 23.4 - - - +
303B ALA* 5.8 6.8 - - - +
306B VAL* 4.6 12.8 - - + +
328B THR 3.9 16.4 - - - +
329B GLN* 2.9 27.6 + - + +
339D ARG* 6.1 0.8 - - - +
340D PRO 3.6 15.0 + - - -
341D THR* 1.3 71.6 - - - +
343D ALA* 1.3 56.6 + - - +
345D GLY* 3.4 2.5 + - - +
346D SER* 2.9 28.9 + - - -
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ARG* 4.3 0.6 - - - +
329B GLN 3.5 20.7 + - - +
330B MET 4.0 6.7 - - - +
343B ALA 3.8 5.5 - - - +
344B GLU* 4.1 13.7 - - + -
347B ASP* 3.4 35.7 - - + +
341D THR* 3.1 6.8 - - - +
342D ARG* 1.3 77.9 - - - +
344D GLU* 1.3 59.2 + - - +
346D SER* 3.4 2.4 + - - -
347D ASP* 2.8 28.4 + - - +
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B THR* 5.0 6.0 + - - +
343B ALA* 4.1 11.0 - - + -
344B GLU* 5.5 3.0 - - + +
329D GLN 4.3 1.4 - - - +
330D MET 3.1 18.3 - - - +
331D LEU* 3.5 12.1 - - + -
332D GLU* 2.9 18.7 + - - +
333D SER* 2.6 51.6 + - - -
340D PRO* 3.6 4.9 - - + +
341D THR* 2.9 27.8 + - - +
343D ALA* 1.3 75.1 - - + +
345D GLY* 1.3 66.6 + - - +
347D ASP* 3.2 6.4 + - - +
348D VAL* 3.1 27.9 + - - +
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Residues in contact with GLY 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ALA* 5.5 7.9 - - - -
307B PHE* 5.4 2.5 - - - -
331D LEU* 4.5 1.7 - - - +
340D PRO* 4.9 4.9 - - - +
341D THR 3.1 12.1 + - - -
342D ARG* 3.8 2.5 - - - -
343D ALA 3.3 0.2 - - - -
344D GLU* 1.3 77.5 - - - +
346D SER* 1.3 63.5 + - - +
348D VAL* 3.4 2.8 + - - +
349D ALA* 3.2 23.6 + - - +
381D ILE* 3.8 24.0 - - - +
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Residues in contact with SER 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 3.7 7.2 + - - -
307B PHE* 4.7 12.3 - - - +
310B GLN* 5.1 6.3 + - - -
347B ASP* 2.6 34.5 + - - -
350B ASN* 4.9 0.5 - - - +
342D ARG 2.9 15.0 + - - -
343D ALA 3.5 1.3 - - - -
345D GLY* 1.3 77.2 - - - +
347D ASP* 1.3 61.4 + - - +
349D ALA* 3.6 5.3 + - - +
350D ASN* 2.9 43.8 + - - +
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Residues in contact with ASP 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ALA* 3.4 28.1 - - + +
346B SER* 2.6 24.7 + - - -
347B ASP 5.3 0.4 - - - +
294D ARG* 2.4 46.5 + - - -
310D GLN* 5.3 1.0 + - - -
330D MET* 3.6 14.2 - - - +
343D ALA 2.8 20.1 + - - +
344D GLU* 3.2 6.5 + - - +
346D SER* 1.3 75.7 - - - +
348D VAL* 1.3 62.3 + - - +
350D ASN* 3.3 2.4 + - - +
351D ALA* 3.0 21.0 + - - +
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Residues in contact with VAL 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D MET* 3.6 28.0 - - + -
331D LEU* 4.1 20.4 - - + -
344D GLU 3.1 13.3 + - - +
345D GLY 3.8 2.5 - - - +
347D ASP* 1.3 78.1 - - - +
349D ALA* 1.3 64.0 + - - +
351D ALA* 3.0 13.9 + - - +
352D VAL* 3.2 14.0 + - + +
359D ILE* 4.0 28.3 - - + -
378D GLN* 4.3 9.2 - - + +
381D ILE* 3.6 30.3 - - + -
382D ALA 4.6 3.6 - - - +
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Residues in contact with ALA 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PHE* 3.5 50.3 - - + -
345D GLY 3.2 12.6 + - - +
346D SER 4.0 3.4 - - - +
348D VAL* 1.3 78.0 - - - +
350D ASN* 1.3 59.7 + - - +
352D VAL* 3.3 5.1 + - - +
353D LEU* 2.9 32.3 + - - +
381D ILE* 3.5 10.0 - - + +
385D ALA* 3.6 7.4 - - - +
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Residues in contact with ASN 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PHE* 5.7 1.0 - - - +
310B GLN* 6.1 0.8 - - - +
311B LYS* 3.1 36.2 + - - +
346B SER* 5.0 0.7 - - - +
350B ASN* 3.4 45.4 - - - +
354B ASP* 5.6 0.6 + - - -
310D GLN* 5.1 1.3 - - - +
311D LYS* 5.5 0.2 + - - -
346D SER* 2.9 37.2 + - - +
347D ASP 3.8 2.9 - - - +
349D ALA* 1.3 77.7 - - - +
351D ALA* 1.3 56.1 + - - +
353D LEU* 3.8 7.2 - - - +
354D ASP* 2.7 45.1 + - - +
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D GLN* 4.1 8.7 - - - +
326D CYS* 4.0 23.8 - - + -
330D MET* 3.8 20.2 - - + -
347D ASP* 3.0 13.0 + - - +
348D VAL 3.0 10.1 + - - +
350D ASN* 1.3 73.6 - - - +
352D VAL* 1.3 66.0 + - - +
354D ASP* 3.4 8.2 - - - +
355D GLY 3.2 5.0 + - - -
356D ALA* 3.1 26.7 + - + +
359D ILE* 4.2 6.1 - - + -
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Residues in contact with VAL 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D THR* 3.7 22.7 - - + +
348D VAL* 3.2 12.0 + - + +
349D ALA 3.5 7.4 - - - +
351D ALA* 1.3 77.9 - - - +
353D LEU* 1.3 54.8 + - - +
355D GLY* 2.7 21.7 + - - -
356D ALA* 4.5 4.0 - - - +
359D ILE* 4.4 8.1 - - + -
382D ALA* 4.0 22.2 - - + +
385D ALA* 3.6 20.0 - - + -
386D GLU* 3.7 22.7 - - + +
389D ILE* 4.5 1.0 - - + +
467D ARG* 2.8 35.1 + - - +
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Residues in contact with LEU 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B MET* 5.9 0.3 - - - +
307B PHE* 4.1 11.4 - - + -
311B LYS* 3.6 37.7 - - + +
349D ALA 2.9 20.3 + - - +
350D ASN* 3.8 11.4 - - - +
352D VAL* 1.3 70.8 - - - +
354D ASP* 1.3 66.0 + - - +
355D GLY* 3.0 3.1 + - - -
385D ALA* 3.6 26.5 - - + +
388D ALA* 3.8 25.8 - - + +
389D ILE* 3.8 14.5 - - + +
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Residues in contact with ASP 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B MET* 4.0 26.7 - - - +
350B ASN* 5.5 0.5 + - - -
310D GLN* 3.0 26.3 + - - -
311D LYS* 2.6 50.1 + - + +
314D ILE* 3.4 27.7 - - + +
318D ASN* 4.2 2.9 + - - -
350D ASN* 2.7 27.1 + - - +
351D ALA 3.4 7.9 - - - +
353D LEU* 1.3 74.1 - - - +
355D GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ILE* 3.2 5.7 - - - +
318D ASN* 3.0 32.5 - - - +
324D VAL* 4.1 0.7 - - - +
352D VAL 2.7 14.6 + - - -
353D LEU 3.0 2.2 - - - -
354D ASP* 1.3 80.7 - - - +
356D ALA* 1.3 58.9 + - - +
357D ASP 4.0 0.2 + - - -
389D ILE* 6.0 0.7 - - - -
394D LEU* 6.3 2.9 - - - -
445D ARG* 3.2 11.9 + - - -
467D ARG* 3.4 11.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il